{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:30Z","timestamp":1772138070659,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,9]],"date-time":"2024-12-09T00:00:00Z","timestamp":1733702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030_197514"],"award-info":[{"award-number":["310030_197514"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. With current technologies such as VisiumHD, thousands of genes can be detected across millions of spots (also called cells or bins depending on the technologies). Building upon the metacell concept, we present a workflow, called SuperSpot, to combine adjacent and transcriptomically similar spots into \u201cmetaspots\u201d. The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptomic similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution. We demonstrate that metaspots reduce the size and sparsity of spatial transcriptomic data and facilitate the analysis of large datasets generated with the most recent technologies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SuperSpot is an R package available at https:\/\/github.com\/GfellerLab\/SuperSpot and archived on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.14222088). The code to reproduce the figures is available at https:\/\/github.com\/GfellerLab\/SuperSpot\/tree\/main\/figures (https:\/\/doi.org\/10.5281\/zenodo.14222088).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae734","type":"journal-article","created":{"date-parts":[[2024,12,6]],"date-time":"2024-12-06T07:26:26Z","timestamp":1733469986000},"source":"Crossref","is-referenced-by-count":2,"title":["SuperSpot: coarse graining spatial transcriptomics data into metaspots"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7834-3992","authenticated-orcid":false,"given":"Matei","family":"Teleman","sequence":"first","affiliation":[{"name":"Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , Lausanne, Lausanne 1015,","place":["Switzerland"]},{"name":"Agora Cancer Research Center , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Cancer Center Leman (SCCL) ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aur\u00e9lie A G","family":"Gabriel","sequence":"additional","affiliation":[{"name":"Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , Lausanne, Lausanne 1015,","place":["Switzerland"]},{"name":"Agora Cancer Research Center , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Cancer Center Leman (SCCL) ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L\u00e9onard","family":"H\u00e9rault","sequence":"additional","affiliation":[{"name":"Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , Lausanne, Lausanne 1015,","place":["Switzerland"]},{"name":"Agora Cancer Research Center , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Cancer Center Leman (SCCL) ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3952-0930","authenticated-orcid":false,"given":"David","family":"Gfeller","sequence":"additional","affiliation":[{"name":"Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , Lausanne, Lausanne 1015,","place":["Switzerland"]},{"name":"Agora Cancer Research Center , Lausanne 1011,","place":["Switzerland"]},{"name":"Swiss Cancer Center Leman (SCCL) ,","place":["Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,9]]},"reference":[{"key":"2025011223411923400_btae734-B1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/s13059-019-1812-2","article-title":"MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions","volume":"20","author":"Baran","year":"2019","journal-title":"Genome Biol"},{"key":"2025011223411923400_btae734-B2","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s13059-022-02667-1","article-title":"Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis","volume":"23","author":"Ben-Kiki","year":"2022","journal-title":"Genome Biol"},{"key":"2025011223411923400_btae734-B3","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/s44320-024-00045-6","article-title":"Building and analyzing metacells in single-cell genomics data","volume":"20","author":"Bilous","year":"2024","journal-title":"Mol Syst Biol"},{"key":"2025011223411923400_btae734-B4","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1186\/s12859-022-04861-1","article-title":"Metacells untangle large and complex single-cell transcriptome networks","volume":"23","author":"Bilous","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2025011223411923400_btae734-B5","doi-asserted-by":"crossref","first-page":"aaa6090","DOI":"10.1126\/science.aaa6090","article-title":"Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"2025011223411923400_btae734-B6","doi-asserted-by":"crossref","first-page":"066111","DOI":"10.1103\/PhysRevE.70.066111","article-title":"Finding community structure in very large networks","volume":"70","author":"Clauset","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"2025011223411923400_btae734-B7","author":"CosMx SMI Human Pancreas FFPE Dataset","year":"2024"},{"key":"2025011223411923400_btae734-B8","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1038\/s41467-022-29439-6","article-title":"Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder","volume":"13","author":"Dong","year":"2022","journal-title":"Nat Commun"},{"key":"2025011223411923400_btae734-B9","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1186\/s12967-023-04150-2","article-title":"Advances in spatial transcriptomics and related data analysis strategies","volume":"21","author":"Du","year":"2023","journal-title":"J Transl Med"},{"key":"2025011223411923400_btae734-B10","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol"},{"key":"2025011223411923400_btae734-B11","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2025011223411923400_btae734-B12","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1038\/s41587-022-01483-z","article-title":"High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging","volume":"40","author":"He","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025011223411923400_btae734-B13","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1093\/nar\/gkac219","article-title":"Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025011223411923400_btae734-B14","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41467-023-36796-3","article-title":"Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST","volume":"14","author":"Long","year":"2023","journal-title":"Nat Commun"},{"key":"2025011223411923400_btae734-B15","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41593-020-00787-0","article-title":"Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex","volume":"24","author":"Maynard","year":"2021","journal-title":"Nat Neurosci"},{"key":"2025011223411923400_btae734-B16","doi-asserted-by":"crossref","first-page":"100498","DOI":"10.1016\/j.crmeth.2023.100498","article-title":"hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data","volume":"3","author":"Morabito","year":"2023","journal-title":"Cell Rep Methods"},{"key":"2025011223411923400_btae734-B17","doi-asserted-by":"publisher","first-page":"A1620","DOI":"10.1136\/jitc-2023-SITC2023.1457","article-title":"1457 Visium HD enables spatially resolved, single-cell scale resolution mapping of FFPE human breast cancer tissue","volume":"11","author":"Nagendran","year":"2023","journal-title":"J Immunother Cancer"},{"key":"2025011223411923400_btae734-B18","doi-asserted-by":"crossref","first-page":"2206939","DOI":"10.1002\/advs.202206939","article-title":"Spatial transcriptomics: technical aspects of recent developments and their applications in neuroscience and cancer research","volume":"10","author":"Park","year":"2023","journal-title":"Adv Sci"},{"key":"2025011223411923400_btae734-B19","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1038\/s41587-023-01716-9","article-title":"SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data","volume":"41","author":"Persad","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025011223411923400_btae734-B20","doi-asserted-by":"crossref","first-page":"btae546","DOI":"10.1093\/bioinformatics\/btae546","article-title":"Bin2cell reconstructs cells from high resolution Visium HD data","volume":"40","author":"Pola\u0144ski","year":"2024","journal-title":"Bioinformatics"},{"key":"2025011223411923400_btae734-B21","first-page":"284","author":"Pons","year":"2005"},{"key":"2025011223411923400_btae734-B22","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1126\/science.aaw1219","article-title":"Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution","volume":"363","author":"Rodriques","year":"2019","journal-title":"Science"},{"key":"2025011223411923400_btae734-B23","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/s41586-023-06569-5","article-title":"Spatial atlas of the mouse central nervous system at molecular resolution","volume":"622","author":"Shi","year":"2023","journal-title":"Nature"},{"key":"2025011223411923400_btae734-B24","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1038\/s41467-019-10802-z","article-title":"Accurate estimation of cell-type composition from gene expression data","volume":"10","author":"Tsoucas","year":"2019","journal-title":"Nat Commun"},{"key":"2025011223411923400_btae734-B25","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41588-023-01588-4","article-title":"CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity","volume":"56","author":"Varrone","year":"2024","journal-title":"Nat Genet"},{"key":"2025011223411923400_btae734-B26","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial transcriptomics at subspot resolution with BayesSpace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae734\/61006805\/btae734.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btae734\/61006805\/btae734.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btae734\/61006805\/btae734.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T18:41:44Z","timestamp":1736707304000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae734\/7919601"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,12,9]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae734","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.06.21.599998","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,12,9]]},"article-number":"btae734"}}